Contacts of the helix formed by residues 246 - 259 (chain F) in PDB entry 1G2D
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 246 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D T 3.7 38.7 - - + +
60D A 2.8 50.8 + - - -
61D A 4.2 5.6 + - - +
73E T 4.5 2.8 - - - +
224F THR* 3.6 29.7 - - + +
227F ARG* 4.7 0.4 - - - +
235F PHE* 3.6 16.2 - - - +
244F PHE* 3.4 1.9 - - - +
245F SER* 1.3 90.2 + - - +
247F HIS* 1.3 65.5 + - - +
248F THR* 3.2 4.7 - - - +
249F GLY* 3.2 5.6 + - - +
250F LEU* 3.1 19.8 + - - +
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Residues in contact with HIS 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E T 4.5 1.8 - - + -
72E T 3.4 79.4 + + + +
73E T 3.3 25.6 - - + +
235F PHE* 3.7 30.9 - + + -
246F GLN* 1.3 74.6 - - - +
248F THR* 1.3 63.0 + - - +
250F LEU* 3.3 4.4 + - - +
251F ASN* 3.1 44.0 + - - -
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Residues in contact with THR 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D T 3.5 20.9 - - - +
73E T 3.3 19.0 + - - +
74E T 2.7 42.2 + - + +
75E A 3.8 4.9 - - - +
246F GLN* 3.2 7.9 + - - +
247F HIS* 1.3 77.8 - - - +
249F GLY* 1.3 58.0 + - - +
251F ASN* 3.1 8.8 + - + +
252F GLN* 2.9 45.7 + - + +
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Residues in contact with GLY 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D T 5.0 1.4 + - - -
58D A 5.5 0.9 - - - -
59D T 4.2 12.4 - - - +
244F PHE* 4.0 18.0 - - - -
246F GLN* 3.2 14.9 + - - +
248F THR* 1.3 77.3 - - - +
250F LEU* 1.3 60.5 + - - +
252F GLN* 3.6 17.0 + - - +
253F HIS* 3.1 24.8 + - - +
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Residues in contact with LEU 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235F PHE* 4.1 24.7 - - + -
236F GLN 3.7 16.8 - - - +
237F CYS* 3.7 32.8 - - + +
244F PHE* 3.8 20.9 - - + +
246F GLN 3.1 11.8 + - - +
247F HIS* 3.7 8.3 - - - +
249F GLY* 1.3 73.9 - - - +
251F ASN* 1.3 62.1 + - - +
253F HIS* 4.3 0.9 - - + -
254F ILE* 2.8 57.4 + - + +
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Residues in contact with ASN 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E T 4.3 8.0 + - - +
247F HIS* 3.1 43.6 + - - +
248F THR* 3.1 12.1 + - + +
250F LEU* 1.3 80.1 - - - +
252F GLN* 1.3 65.8 + - - +
254F ILE* 3.5 19.6 + - - +
255F ARG* 3.4 36.4 + - - +
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Residues in contact with GLN 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D C 5.8 0.3 - - - +
57D T 3.5 35.9 + - + +
58D A 2.8 48.1 + - - +
75E A 4.1 1.4 + - - -
248F THR* 2.9 34.1 + - + +
249F GLY* 3.7 14.4 + - - +
251F ASN* 1.3 75.1 - - + +
253F HIS* 1.3 64.2 + - - +
255F ARG* 3.3 34.5 + - - +
256F THR* 4.0 6.9 + - - +
273F ALA* 5.5 0.9 - - - +
274F THR* 4.0 19.4 - - + +
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Residues in contact with HIS 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D T 2.8 32.7 + - - +
237F CYS* 3.6 10.7 - - + +
240F CYS* 3.6 9.6 - - - -
242F ARG* 4.6 7.4 + - + -
244F PHE* 3.1 36.9 - + + -
249F GLY 3.1 16.1 + - - +
250F LEU* 3.6 5.2 - - + +
252F GLN* 1.3 77.3 - - - +
254F ILE* 1.3 65.3 + - - +
255F ARG 3.0 2.2 - - - -
256F THR* 2.8 34.1 + - - -
257F HIS* 3.3 7.0 + + - -
305F ZN 2.1 36.5 - - - -
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Residues in contact with ILE 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F CYS* 4.7 11.7 - - - -
238F ARG 6.2 0.7 - - - +
239F ILE* 5.6 5.8 - - + -
250F LEU* 2.8 54.7 + - + +
251F ASN* 3.9 15.7 - - - +
252F GLN 3.4 0.4 - - - -
253F HIS* 1.3 75.7 - - - +
255F ARG* 1.3 62.5 + - + +
257F HIS* 3.1 20.9 + - + +
258F THR* 3.2 24.6 + - + +
260F GLU* 6.0 0.7 - - - +
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Residues in contact with ARG 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F ASN* 3.4 28.8 + - - +
252F GLN* 3.4 28.5 - - - +
253F HIS 3.0 1.2 + - - -
254F ILE* 1.3 75.0 - - + +
256F THR* 1.3 57.0 + - + +
257F HIS 3.0 2.5 - - - -
258F THR* 3.5 8.1 - - - +
259F GLY* 2.7 33.7 + - - -
260F GLU* 3.5 42.6 + - + +
262F PRO* 3.9 9.6 - - - +
263F PHE* 3.9 20.3 - - - -
273F ALA* 2.9 40.1 + - + +
274F THR* 4.0 7.1 - - - +
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Residues in contact with THR 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D C 3.6 48.3 + - - +
57D T 3.9 15.9 - - - +
252F GLN 4.0 9.4 - - - +
253F HIS* 2.8 32.3 + - - +
255F ARG* 1.3 77.0 - - - +
257F HIS* 1.3 67.1 + - - +
259F GLY* 4.3 2.9 + - - -
273F ALA* 6.5 0.2 - - + -
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Residues in contact with HIS 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F CYS* 3.5 11.6 - - - -
239F ILE* 3.8 41.1 - - + +
240F CYS* 4.3 9.6 - - + -
253F HIS* 3.3 13.4 + + - -
254F ILE* 3.1 13.0 + - - +
255F ARG 3.0 0.2 - - - -
256F THR* 1.3 85.9 + - - +
258F THR* 1.3 65.3 + - + +
259F GLY* 3.4 0.7 + - - -
305F ZN 2.1 36.4 - - - -
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Residues in contact with THR 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239F ILE* 5.6 4.3 - - + -
254F ILE* 3.2 21.5 + - + +
255F ARG* 3.5 9.9 - - - -
257F HIS* 1.3 79.1 - - + +
259F GLY* 1.3 63.0 + - - +
260F GLU* 3.3 24.3 + - - +
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Residues in contact with GLY 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255F ARG 2.7 19.5 + - - -
256F THR 4.3 2.9 - - - -
257F HIS 3.4 3.0 + - - -
258F THR* 1.3 75.1 - - - +
260F GLU* 1.3 62.4 + - - +
261F LYS* 3.6 17.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il